An analysis of core deformations in protein superfamilies.

ABSTRACT: An analysis is presented on how structural cores modify their shape across homologous proteins, and whether or not a relationship exists between these structural changes and the vibrational normal modes that proteins experience as a result of the topological constraints imposed by the fold. A set of 35 representative, well-populated protein families is studied. The evolutionary directions of deformation are obtained by using multiple structural alignments to superimpose the structures and extract a conserved core, together with principal components analysis to extract the main deformation modes from the three-dimensional superimposition. In parallel, a low-resolution normal mode analysis technique is employed to study the properties of the mechanical core plasticity of these same families.

SUBMITTER: Leo-Macias A 

PROVIDER: S-EPMC1305131 | biostudies-literature | 2005 Feb

REPOSITORIES: biostudies-literature